Climate warming is predicted to cause boreal forests in the Boundary Waters Canoe Area Wilderness (BWCAW), Minnesota, to shift to savanna and/or temperate forest in the next century. Invasive earthworms, exotic tree pests, and deer overabundance will magnify the impacts of warmer temperatures. Seldom do we assess potential threats to ecosystem and wilderness integrity in a systematic way and develop policy and management strategies ahead of time to mitigate the situation. Debates on several issues involving wilderness users, managers, and scientists need to be resolved for the BWCAW. These include whether, when, and how to: (1) use fire; (2) restore tree species to wilderness areas lost through human actions (e.g., logging of white pine (Pinus strobus L.) that occurred before wilderness designation and potential loss of ash species from the introduced pest emerald ash borer (Agrilus planipennis Fairmaire)); (3) manage the potential overabundance of deer that threaten reproduction of some tree species; (4) facilitate (or prevent) migration of new tree species currently native south of the wilderness; (5) employ local (within wilderness) or regional assisted migration for species that cannot migrate fast enough on their own to keep up with climate change; and (6) manage invasive species. Some of these activities would not be allowed under the wilderness laws of 1964 and 1978, and may be difficult to enact or limited in effectiveness. Major change in forests of the BWCAW is a certainty, and facilitation of a ‘graceful transition’ to native species rather than exotic species is desirable.